User: angrypigeon

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angrypigeon120
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Posts by angrypigeon

<prev • 66 results • page 1 of 7 • next >
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Separate Genome into Tiers
... I've seen the genome separated into tiers based on functionality; something like Tier I: coding and Tier III: non-coding, non-repeating, non-conserved. Is there a way to match these classifications up with actual genomic locations? I am working specifically with mouse at the moment but it would be g ...
genome written 26 days ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This actually works pretty well. I grabbed a targeted region of sequence from UCSC with something like this: wget -O - http://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=%s:%s,%s >> locs\n' % (chrom, low, high) Then used this in UCSC BLAT to find the orthologous region within mouse. (Th ...
written 6 weeks ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This is what I don't know how to do. I can see how the mouse gene can be accessed, but then how to target a particular hotspot within that region and identify its coordinates? ...
written 6 weeks ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This is an interesting resource, but I'm still not quite sure how this would help me target a particular sequence. The reference you point to seems to do a nice job of identifying the entire gene region, but how would I target a particular hotspot within the given gene? ...
written 6 weeks ago by angrypigeon120
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How to get orthologous sequence
... Is there a nice way to get orthologous sequence of a particular gene locus? As an example of what I'm trying to do: Say I have the gene CTNNB1 that is commonly mutated in humans at chr3:41266124. Now, I would like to convert this location to the mouse genome and get the surrounding gDNA sequence. ...
genome gene written 6 weeks ago by angrypigeon120 • updated 6 weeks ago by lieven.sterck3.0k
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Get gene names from ensembl ID or gene region
... I have some RNASeq data that has fpkm values labeled with genome positions like `chr7 52823165 52830546` Ensembl IDs like `ENSMUST00000143813` and gene symbols like `0610005C13Rik`. Is there a good programmatic way in python to get gene names from any of this data so I can match up the fpkm values w ...
ensembl rna-seq python written 8 weeks ago by angrypigeon120 • updated 8 weeks ago by Alex Reynolds26k
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Comment: C: Label fastq reads
... Right, I was thinking that there might be a way to track this information in an associated file, but if I am doing this pre-alignment, I do not know how to associate the read information with output variants. ...
written 5 months ago by angrypigeon120
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Comment: C: Label fastq reads
... The goal is a bit complicated, but essentially I have barcoded fastq reads that I am binning together and using for consensus sequence derivation. I would like to retain parts of the information in the binned reads such as percent sequence agreement at each position. Then I would be using this infor ...
written 5 months ago by angrypigeon120
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Label fastq reads
... I am deriving some sequencing consensus reads from fastq files, and I would like to keep track of some information during the derivation process, and I'm wondering if there is a good way to do this. To simplify the problem if I have a fastq file with the following read in it, I want to associate som ...
alignment sequencing written 5 months ago by angrypigeon120 • updated 5 months ago by swbarnes24.5k
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Comment: C: Samtools faidx non-zero exit status 217
... Yeah samtools does appear to be working fine. I'll try building a new reference and see if this helps. ...
written 6 months ago by angrypigeon120

Latest awards to angrypigeon

Supporter 6 weeks ago, voted at least 25 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For Reason for Freebayes Calling Multi-base Variants
Popular Question 5 months ago, created a question with more than 1,000 views. For Converting Illumina fastq quality scores to phred
Popular Question 5 months ago, created a question with more than 1,000 views. For Lollipop Plot of Variant Locations
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Converting Illumina fastq quality scores to phred
Popular Question 15 months ago, created a question with more than 1,000 views. For Converting Illumina fastq quality scores to phred
Scholar 23 months ago, created an answer that has been accepted. For A: Running bcbio.rnaseq with correct formula
Scholar 2.1 years ago, created an answer that has been accepted. For A: Running bcbio.rnaseq with correct formula

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